HsaALTA0008402-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000197283 | SYNGAP1
Description
synaptic Ras GTPase activating protein 1 [Source:HGNC Symbol;Acc:11497]
Coordinates
chr6:33412221-33414563:+
Coord C1 exon
chr6:33412221-33412394
Coord A exon
chr6:33414352-33414357
Coord C2 exon
chr6:33414358-33414563
Length
6 bp
Sequences
Splice sites
5' ss Seq
AGGGTACGA
5' ss Score
7.38
3' ss Seq
GTCGTGTGCCCGGCGGGCAGGTG
3' ss Score
5.41
Exon sequences
Seq C1 exon
CATTCTCAGACACCATCCACATTGAACCCCACAATGCCAGCCTCTGAGCGGACAGTGGCCTGGGTCTCCAACATGCCTCACCTGTCGGCTGACATCGAGAGTGCCCACATCGAGCGGGAAGAGTACAAGCTCAAGGAGTACTCAAAATCGATGGATGAGAGCCGGCTGGATAGG
Seq A exon
GTGAAG
Seq C2 exon
GAGTACGAGGAGGAGATTCACTCACTGAAAGAGCGGCTGCACATGTCCAACCGGAAGCTGGAAGAGTATGAGCGGAGGCTGCTGTCCCAGGAAGAACAAACCAGCAAAATCCTGATGCAGTATCAGGCCCGACTGGAGCAGAGTGAGAAGAGGCTAAGGCAGCAGCAGGCAGAGAAGGATTCCCAGATCAAGAGCATCATTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197283-19-22,19-21-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.972 A=NA C2=0.792
Domain overlap (PFAM):
C1:
PF120043=DUF3498=FE(10.1=100)
A:
NA
C2:
PF120043=DUF3498=FE(12.1=100)
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATCGAGCGGGAAGAGTACA
R:
GCCGCTCTTTCAGTGAGTGAA
Band lengths:
105-111
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)